Title: The effects of mismatches on hybridization in DNA microarrays: determination of nearest neighbor parameters
Authors: Hooyberghs, J ×
Van Hummelen, P
Carlon, Enrico #
Issue Date: Apr-2009
Publisher: Oxford univ press
Series Title: Nucleic acids research vol:37 issue:7 pages:1-11
Article number: e53
Abstract: Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called nearest neighbor model, which estimates the hybridization free energy of a given sequence as a sum of dinucleotide terms. Compared with its solution counterparts, hybridization in DNA microarrays may be hindered due to the presence of a solid surface and of a high density of DNA strands. We present here a study aimed at the determination of hybridization free energies in DNA microarrays. Experiments are performed on custom Agilent slides. The solution contains a single oligonucleotide. The microarray contains spots with a perfect matching (PM) complementary sequence and other spots with one or two mismatches (MM) : in total 1006 different probe spots, each replicated 15 times per microarray. The free energy parameters are directly fitted from microarray data. The experiments demonstrate a clear correlation between hybridization free energies in the microarray and in solution. The experiments are fully consistent with the Langmuir model at low intensities, but show a clear deviation at intermediate (non-saturating) intensities. These results provide new interesting insights for the quantification of molecular interactions in DNA microarrays.
ISSN: 0305-1048
Publication status: published
KU Leuven publication type: IT
Appears in Collections:Theoretical Physics Section
× corresponding author
# (joint) last author

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